The flanker will now miss Wales' summer tour of South Africa after it was confirmed he will go under the knife this week.
The British and Irish Lions forward is not the only Wales star suffering with a shoulder complaint.
Warburton joins full-back Leigh Halfpenny - who had successful surgery on his shoulder last week - on the sidelines and both face a spell out.
"Following MRI scans and consultations with specialists, Warburton will have an operation and is expected to miss several months of action," said a Cardiff Blues statement.
"Everybody at Cardiff Blues wishes Sam and Leigh all the best during their rehabilitation."